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Said H, Ratabane J, Erasmus L, Gardee Y, Omar S, Dreyer A, Ismail F, Bhyat Z, Lebaka T, van der Meulen M, Gwala T, Adelekan A, Diallo K, Ismail N. Distribution and Clonality of drug-resistant tuberculosis in South Africa. BMC Microbiol 2021; 21:157. [PMID: 34044775 PMCID: PMC8161895 DOI: 10.1186/s12866-021-02232-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Background Studies have shown that drug-resistant tuberculosis (DR-TB) in South Africa (SA) is clonal and is caused mostly by transmission. Identifying transmission chains is important in controlling DR-TB. This study reports on the sentinel molecular surveillance data of Rifampicin-Resistant (RR) TB in SA, aiming to describe the RR-TB strain population and the estimated transmission of RR-TB cases. Method RR-TB isolates collected between 2014 and 2018 from eight provinces were genotyped using combination of spoligotyping and 24-loci mycobacterial interspersed repetitive-units-variable-number tandem repeats (MIRU-VNTR) typing. Results Of the 3007 isolates genotyped, 301 clusters were identified. Cluster size ranged between 2 and 270 cases. Most of the clusters (247/301; 82.0%) were small in size (< 5 cases), 12.0% (37/301) were medium sized (5–10 cases), 3.3% (10/301) were large (11–25 cases) and 2.3% (7/301) were very large with 26–270 cases. The Beijing genotype was responsible for majority of RR-TB cases in Western and Eastern Cape, while the East-African-Indian-Somalian (EAI1_SOM) genotype accounted for a third of RR-TB cases in Mpumalanga. The overall proportion of RR-TB cases estimated to be due to transmission was 42%, with the highest transmission-rate in Western Cape (64%) and the lowest in Northern Cape (9%). Conclusion Large clusters contribute to the burden of RR-TB in specific geographic areas such as Western Cape, Eastern Cape and Mpumalanga, highlighting the need for community-wide interventions. Most of the clusters identified in the study were small, suggesting close contact transmission events, emphasizing the importance of contact investigations and infection control as the primary interventions in SA. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02232-z.
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Affiliation(s)
- Halima Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa. .,Department of Medical Microbiology, Faculty of Health Science, University of Free State, Bloemfontein, South Africa.
| | - John Ratabane
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Linda Erasmus
- Division of Public Health Surveillance and Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Shaheed Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | | | - Farzana Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Zaheda Bhyat
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Tiisetso Lebaka
- Division of Public Health Surveillance and Response, National Institute of Communicable Diseases, Johannesburg, South Africa
| | - Minty van der Meulen
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Thabisile Gwala
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa
| | - Adeboye Adelekan
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Karidia Diallo
- Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, 1 Moderfontein Road, Sandringham, Johannesburg, 2131, South Africa.,Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
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Trends in Mycobacterium tuberculosis Transmission During a 10-year Period (2006-2016) in the Northwest of Iran by MIRU-VNTR Molecular Typing. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.95891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040782. [PMID: 29673235 PMCID: PMC5923824 DOI: 10.3390/ijerph15040782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI) value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%). By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP), and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%). By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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Riyahi Zaniani F, Moghim S, Mirhendi H, Ghasemian Safaei H, Fazeli H, Salehi M, Nasr Esfahani B. Genetic Lineages of Mycobacterium tuberculosis Isolates in Isfahan, Iran. Curr Microbiol 2016; 74:14-21. [PMID: 27743106 DOI: 10.1007/s00284-016-1145-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
In this study, we aimed to identify the genetic lineages of Mycobacterium tuberculosis isolates in Isfahan via the mycobacterial interspersed repetitive-unit-variable number tandem repeat typing method based on 15 loci. Forty-nine M. tuberculosis isolates were collected between 2013 and 2015 from Tuberculosis patients in Mollahadi Sabzevari Tuberculosis Center in Isfahan. All isolates were typed by 15-locus MIRU-VNTR typing. The highest percentage of isolates, 44.89 % (22/49), belonged to the Euro-American lineage, while the frequencies of the East-African-Indian, East-Asian, and Indo-Oceanic lineages were 28.57 % (14/49), 24.4 % (12/49), and 2.04 % (1/49), respectively. Among the 22 isolates of the Euro-American lineage, those belonging to the NEW-1 sub-lineage were most prevalent (24.4 %). Approximately, the same proportion of isolates belonging to the Delhi/CAS, Beijing, and NEW-1 sub-lineages were identified in Iranian and Afghan immigrant patients. The Delhi/CAS and Beijing sub-lineage isolates were prevalent among patients who had been previously treated for TB. Results showed that all of the 49 MIRU-VNTR patterns were unique and the clustering rate of the 15-locus MIRU-VNTR was 0.0 (minimum recent transmission). The results of this study show that the lineages of M. tuberculosis isolates in Isfahan are similar to those reported in the Eastern Mediterranean region (indicative of the epidemiological relationship between the countries in the region). The low clustering rate in our results reveals that transmission of tuberculosis in Isfahan is, in most cases, a reactivation of previous tuberculosis infection and the role of recently transmitted disease is minor.
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Affiliation(s)
- Fatemeh Riyahi Zaniani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Sharareh Moghim
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Hossein Mirhendi
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Hajieh Ghasemian Safaei
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Hossein Fazeli
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran
| | - Mahshid Salehi
- Regional Tuberculosis Reference Laboratories in Esfahan, Esfahān, Iran
| | - Bahram Nasr Esfahani
- Department of Microbiology, Faculty of Medicine, Isfahan University of Medical Sciences, Esfahān, Iran.
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Abstract
RATIONALE HIV-associated tuberculosis remains a major health problem among the gold-mining workforce in South Africa. We postulate that high levels of recent transmission, indicated by strain clustering, are fueling the tuberculosis epidemic among gold miners. OBJECTIVES To combine molecular and epidemiologic data to describe Mycobacterium tuberculosis genetic diversity, estimate levels of transmission, and examine risk factors for clustering. METHODS We conducted a cross-sectional study of culture-positive M. tuberculosis isolates in 15 gold mine shafts across three provinces in South Africa. All isolates were subject IS6110-based restriction fragment length polymorphisms, and we performed spoligotyping analysis and combined it with basic demographic and clinical information. MEASUREMENTS AND MAIN RESULTS Of the 1,602 M. tuberculosis patient isolates, 1,240 (78%) had genotyping data available for analysis. A highly diverse bacillary population was identified, comprising a total of 730 discrete genotypes. Four genotypic families (Latin American Mediterranean spoligotype family; W-Beijing; AH or X; and T1-T4) accounted for over 50% of all strains. Overall, 45% (560/1,240) of strains were genotypically clustered. The minimum estimate for recent transmission (n - 1 method) was 32% (range, 27-34%). There were no individual-level risk factors for clustering, apart from borderline evidence for being non-South African and having self-reported HIV infection. CONCLUSIONS The high M. tuberculosis genetic diversity and lack of risk factors for clustering are indicative of a universal risk for disease among gold miners and likely mixing with nonmining populations. Our results underscore the urgent need to intensify interventions to interrupt transmission across the entire gold-mining workforce in South Africa.
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Bouklata N, Supply P, Jaouhari S, Charof R, Seghrouchni F, Sadki K, El Achhab Y, Nejjari C, Filali-Maltouf A, Lahlou O, El Aouad R. Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco. PLoS One 2015; 10:e0135695. [PMID: 26285026 PMCID: PMC4540494 DOI: 10.1371/journal.pone.0135695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/26/2015] [Indexed: 01/27/2023] Open
Abstract
Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco, and could therefore be used to better study tuberculosis transmission in a population-based, multi-year sample context.
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Affiliation(s)
- Nada Bouklata
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
- * E-mail:
| | - Philip Supply
- INSERMU1018, Lille, France
- CNRS UMR8204, Lille, France
- Center for Infection and Immunity of Lille (CIIL), Institut Pasteur de Lille, France
- Université de Lille, Lille, France
- Genoscreen, Lille, France
| | - Sanae Jaouhari
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Reda Charof
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Fouad Seghrouchni
- Laboratory of Cell Immunology, Department of Immunology, National Institute of Hygiene, Rabat, Morocco
| | - Khalid Sadki
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Youness El Achhab
- Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes, Morocco
| | - Chakib Nejjari
- Department of Epidemiology and Public Health, Faculty of Medicine and Pharmacy of Fes, Sidi Mohamed Ben Abdillah University, Fes, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco
| | - Ouafae Lahlou
- National Tuberculosis Reference Laboratory, National Institute of Hygiene, Rabat, Morocco
| | - Rajae El Aouad
- School of Public Health and Management System Health, University Mohamed VI of Sciences and Health, Casablanca, Morocco
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Pouseele H, Supply P. Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Diversity and evolution of Mycobacterium tuberculosis: moving to whole-genome-based approaches. Cold Spring Harb Perspect Med 2014; 4:a021188. [PMID: 25190252 DOI: 10.1101/cshperspect.a021188] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Genotyping of clinical Mycobacterium tuberculosis complex (MTBC) strains has become a standard tool for epidemiological tracing and for the investigation of the local and global strain population structure. Of special importance is the analysis of the expansion of multidrug (MDR) and extensively drug-resistant (XDR) strains. Classical genotyping and, more recently, whole-genome sequencing have revealed that the strains of the MTBC are more diverse than previously anticipated. Globally, several phylogenetic lineages can be distinguished whose geographical distribution is markedly variable. Strains of particular (sub)lineages, such as Beijing, seem to be more virulent and associated with enhanced resistance levels and fitness, likely fueling their spread in certain world regions. The upcoming generalization of whole-genome sequencing approaches will expectedly provide more comprehensive insights into the molecular and epidemiological mechanisms involved and lead to better diagnostic and therapeutic tools.
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Boritsch EC, Supply P, Honoré N, Seeman T, Stinear TP, Brosch R. A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent. Mol Microbiol 2014; 93:835-52. [DOI: 10.1111/mmi.12720] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Eva C. Boritsch
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Philip Supply
- INSERM U1019; Lille France
- CNRS UMR 8204; Lille France
- University of Lille Nord de France; Lille France
- Institut Pasteur de Lille; Center for Infection and Immunity of Lille; Lille France
| | - Nadine Honoré
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Torsten Seeman
- Victorian Bioinformatics Consortium; Monash University; Clayton Victoria Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology; University of Melbourne; Parkville Victoria Australia
| | - Roland Brosch
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
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Combination of multiplex PCR with denaturing high-performance liquid chromatography for rapid detection of Mycobacterium genus and simultaneous identification of the Mycobacterium tuberculosis complex. Diagn Microbiol Infect Dis 2013; 77:53-7. [DOI: 10.1016/j.diagmicrobio.2013.06.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/22/2013] [Accepted: 06/01/2013] [Indexed: 11/17/2022]
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Lu B, Zhao P, Liu B, Dong H, Yu Q, Zhao X, Wan K. Genetic diversity of Mycobacterium tuberculosis isolates from Beijing, China assessed by Spoligotyping, LSPs and VNTR profiles. BMC Infect Dis 2012; 12:372. [PMID: 23259861 PMCID: PMC3583687 DOI: 10.1186/1471-2334-12-372] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Accepted: 12/13/2012] [Indexed: 11/28/2022] Open
Abstract
Background Tuberculosis is one of the most infectious diseases in the world. Molecular typing methods such as spoligotyping, and VNTR (variable number tandem repeats), IS6110 in the NTF region and LSP (large sequence polymorphisms) analysis are generally useful tools for the resolution of various issues related to the classical epidemiology of Mycobacterium tuberculosis (M. tuberculosis). Methods To determine the transmission characteristics of M. tuberculosis strains isolated in Beijing, China, and their genetic relationships, especially those among Beijing family strains, 260 M. tuberculosis strains isolated from patients presenting pulmonary tuberculosis were analyzed by spoligotyping, and by examining 22 VNTR loci and the presence/absence of IS6110 in the NTF region, RD105 and RD181. Results 81% (211 strains) of the isolates studied were Beijing family strains, 174 (82.5%) of which were identified as modern Beijing strains based on the presence of IS6110 upstream of the NTF region. RD181 was intact in 9 of the other 37 (17.5%) ancestral Beijing strains. The percentage of Beijing family strains in this study was consistent with previous reports. There are many differences, however, in allele diversity among VNTR loci between reports on strains from different areas. Conclusions The Beijing family is the most prevalent genotype in Beijing city and the predominance of Beijing family strains has not altered in almost twenty years. Differences in the alleles and discrimination ability of VNTR loci between different regions is likely due to population differences in the regions where these M. tuberculosis strains were isolated or to differences in sampling times.
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Affiliation(s)
- Bing Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention & National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, PR China
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Sirgel FA, Warren RM, Streicher EM, Victor TC, van Helden PD, Böttger EC. gyrA mutations and phenotypic susceptibility levels to ofloxacin and moxifloxacin in clinical isolates of Mycobacterium tuberculosis. J Antimicrob Chemother 2012; 67:1088-93. [PMID: 22357804 DOI: 10.1093/jac/dks033] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To compare mutations in the quinolone resistance-determining region of the gyrA gene and flanking sequences with the MICs of ofloxacin and moxifloxacin for Mycobacterium tuberculosis. METHODS The presence of mutations in 177 drug-resistant M. tuberculosis isolates was determined by DNA sequencing and the MICs quantified by MGIT 960. RESULTS Single nucleotide polymorphisms were detected at codons 94 (n = 30), 90 (n = 12), 91 (n = 3), 89 (n = 1), 88 (n = 1) and 80 (n = 1). Four isolates with double mutations D94G plus A90V (n = 2) and D94G plus D94N (n = 2) reflect mixed populations. Agreement between genotypic and phenotypic susceptibility was high (≥97%) for both drugs. Mutant isolates had an MIC(50) of 8.0 mg/L and an MIC(90) of >10 mg/L for ofloxacin compared with an MIC(50) and MIC(90) of 2.0 mg/L for moxifloxacin. Codons 94 and 88 were linked to higher levels of fluoroquinolone resistance compared with codons 90, 91 and 89. The MIC distributions for the wild-type isolates ranged from ≤0.5 to 2.0 mg/L for ofloxacin and from ≤0.125 to 0.25 mg/L for moxifloxacin. However, 96% of the isolates with genetic alterations had MICs ≤2.0 mg/L for moxifloxacin, which is within its achievable serum levels. CONCLUSIONS This study provides quantitative evidence that the addition of moxifloxacin to extensively drug-resistant tuberculosis (XDR-TB) regimens based on a clinical breakpoint of 2.0 mg/L has merit. The use of moxifloxacin in the treatment of multidrug-resistant tuberculosis may prevent the acquisition of additional mutations and development of XDR-TB.
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Affiliation(s)
- Frederick A Sirgel
- DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Science, Stellenbosch University, Stellenbosch, South Africa.
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Faksri K, Drobniewski F, Nikolayevskyy V, Brown T, Prammananan T, Palittapongarnpim P, Prayoonwiwat N, Chaiprasert A. Genetic diversity of the Mycobacterium tuberculosis Beijing family based on IS6110, SNP, LSP and VNTR profiles from Thailand. INFECTION GENETICS AND EVOLUTION 2011; 11:1142-9. [PMID: 21515409 DOI: 10.1016/j.meegid.2011.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 04/04/2011] [Accepted: 04/08/2011] [Indexed: 01/23/2023]
Abstract
The Beijing family of Mycobacterium tuberculosis (MTB) has been shown to be highly virulent and is associated with tuberculosis outbreaks and drug resistance. To explore the evolutionary pathway of this genotype, 165 epidemiologically unlinked Beijing MTB isolates from Thailand were characterized based on IS6110, variable number of tandem repeats (VNTRs), region of differences (RDs) and single nucleotide polymorphisms (SNPs). Analysis based on VNTRs showed that 7 VNTRs were phylogenetically informative loci. Three of the seven VNTRs, 4156, 1982 and 1955, were promising markers for defining ancestral and modern Beijing sublineages. The evolutionary history of Beijing sublineages based on VNTR profiles showed dynamic changes in the repeat number, which also correlated with specific SNP STs. We constructed a refined, comprehensive phylogenetic tree based on multiple genetic markers from the Beijing strains from Thailand and combined the data with previous studies that were performed in South Africa and Japan. The phylogenetic tree showed how the modern Beijing and W-Beijing strains evolved from ancestral Beijing strains. The points at which the RD150 deletion occurred repeatedly were also demonstrated. The evolutionary scheme showed that most events were concordant with the SNP STs. Nevertheless, some SNPs used for sub-typing the Beijing family of MTB may not be irreversible, unique events.
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Affiliation(s)
- Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Prannok Road, Siriraj Hospital Siriraj Bangkoknoi, Bangkok 10700, Thailand
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Rovina N, Karabela S, Constantoulakis P, Michou V, Konstantinou K, Sgountzos V, Roussos C, Poulakis N. MIRU-VNTR typing of drug-resistant tuberculosis isolates in Greece. Ther Adv Respir Dis 2011; 5:229-36. [DOI: 10.1177/1753465811402120] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The increasing immigration rate in Greece from countries with a high prevalence of Mycobacterium tuberculosis (MTB) and multidrug-resistant tuberculosis (MDR-TB) may have an impact οn the number of MDR-TB cases in Greece. The aim of this study was to genotypically characterize the MTB isolates from patients with pulmonary drug-resistant tuberculosis (DR-TB) in Greece, and to determine whether there is any association between the prevalent genotypes and drug resistance. Fifty-three drug-resistant MTB strains isolated from culture specimens of clinical material from native Greeks and immigrant patients with pulmonary tuberculosis were genotyped using the mycobacterial interspersed repetitive units–variable number of tandem repeats (MIRU-VNTR) method. The phylogenetically distinct groups of isolates identified were: the Beijing (34%), the LAM (11%), the Haarlem (24.5%), the Uganda I (9.4%), the Ural (3.8%), the Delhi/CAS (9.4%) and the Cameroon (3.8%) families. Greek patients were more likely to have monoresistant and polyresistant TB with the most prevalent isolates belonging to the Haarlem family. Among foreign-born patients with MDR-TB, the most prevalent genotypes belonged to the Beijing family. MIRU-VNTR rapidly obtained clinically useful genotyping data, by characterizing clonal MTB heterogeneity in the isolated strains. Our results underline the need for more effective antituberculosis control programs in order to control the expansion of DR-TB in Greece.
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Affiliation(s)
- Nikoletta Rovina
- 1st University Pulmonary Department, Medical School, National and Kapodistrian University of Athens ‘SOTIRIA’ District Chest Diseases Hospital, 152 Mesogion Street, 11527 Athens, Greece
| | - Simona Karabela
- National Center of Tuberculosis, Microbiology Department, ‘SOTIRIA’ District Chest Diseases Hospital, 152 Mesogion Street, 11527, Athens, Greece
| | | | | | | | - Vassileios Sgountzos
- Clinic of Multi-drug Resistant Tuberculosis, ‘SOTIRIA’ District Chest Diseases Hospital, 152 Mesogion Street, 11527 Athens, Greece
| | - Charis Roussos
- National and Kapodistrian University of Athens, Pulmonary Department, ‘SOTIRIA’ District Chest Diseases Hospital, 152 Mesogion Street, 11527 Athens, Greece and National and Kapodistrian University of Athens, Department of Critical Care and Pulmonary Services, General Hospital Evangelismos, 3 Ploutarhou Street, 10675 Athens, Greece
| | - Nikolaos Poulakis
- 1st Pulmonary Department, ‘SOTIRIA’ District Chest Diseases Hospital, 152 Mesogion Street, 11527 Athens, Greece
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Cardoso Oelemann M, Gomes HM, Willery E, Possuelo L, Batista Lima KV, Allix-Béguec C, Locht C, Goguet de la Salmonière YOL, Gutierrez MC, Suffys P, Supply P. The forest behind the tree: phylogenetic exploration of a dominant Mycobacterium tuberculosis strain lineage from a high tuberculosis burden country. PLoS One 2011; 6:e18256. [PMID: 21464915 PMCID: PMC3064675 DOI: 10.1371/journal.pone.0018256] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 03/01/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genotyping of Mycobacterium tuberculosis isolates is a powerful tool for epidemiological control of tuberculosis (TB) and phylogenetic exploration of the pathogen. Standardized PCR-based typing, based on 15 to 24 mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) loci combined with spoligotyping, has been shown to have adequate resolution power for tracing TB transmission and to be useful for predicting diverse strain lineages in European settings. Its informative value needs to be tested in high TB-burden countries, where the use of genotyping is often complicated by dominance of geographically specific, genetically homogeneous strain lineages. METHODOLOGY/PRINCIPAL FINDINGS We tested this genotyping system for molecular epidemiological analysis of 369 M. tuberculosis isolates from 3 regions of Brazil, a high TB-burden country. Deligotyping, targeting 43 large sequence polymorphisms (LSPs), and the MIRU-VNTRplus identification database were used to assess phylogenetic predictions. High congruence between the different typing results consistently revealed the countrywide supremacy of the Latin-American-Mediterranean (LAM) lineage, comprised of three main branches. In addition to an already known RDRio branch, at least one other branch characterized by a phylogenetically informative LAM3 spoligo-signature seems to be globally distributed beyond Brazil. Nevertheless, by distinguishing 321 genotypes in this strain population, combined MIRU-VNTR typing and spoligotyping demonstrated the presence of multiple distinct clones. The use of 15 to 24 loci discriminated 21 to 25% more strains within the LAM lineage, compared to a restricted lineage-specific locus set suggested to be used after SNP analysis. Noteworthy, 23 of the 28 molecular clusters identified were exclusively composed of patient isolates from a same region, consistent with expected patterns of mostly local TB transmission. CONCLUSIONS/SIGNIFICANCE Standard MIRU-VNTR typing combined with spoligotyping can reveal epidemiologically meaningful clonal diversity behind a dominant M. tuberculosis strain lineage in a high TB-burden country and is useful to explore international phylogenetical ramifications.
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Affiliation(s)
- Maranibia Cardoso Oelemann
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Harrison M. Gomes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Eve Willery
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Lia Possuelo
- Center of Scientific and Technological Development, Fundação Estadual de Produção e Pesquisa em Saúde, Porto Alegre, Brazil
| | | | - Caroline Allix-Béguec
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Camille Locht
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | | | - Maria Cristina Gutierrez
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- Department of Infection and Epidemiology, Institut Pasteur, Paris, France
| | - Philip Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Philip Supply
- INSERM U1019, Lille, France
- CNRS UMR 8204, Lille, France
- Univ Lille Nord de France, Lille, France
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
- * E-mail:
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17
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Gaffé J, McKenzie C, Maharjan RP, Coursange E, Ferenci T, Schneider D. Insertion Sequence-Driven Evolution of Escherichia coli in Chemostats. J Mol Evol 2011; 72:398-412. [DOI: 10.1007/s00239-011-9439-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/01/2011] [Indexed: 11/30/2022]
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18
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Ioerger TR, Feng Y, Chen X, Dobos KM, Victor TC, Streicher EM, Warren RM, Gey van Pittius NC, Van Helden PD, Sacchettini JC. The non-clonality of drug resistance in Beijing-genotype isolates of Mycobacterium tuberculosis from the Western Cape of South Africa. BMC Genomics 2010; 11:670. [PMID: 21110864 PMCID: PMC3091785 DOI: 10.1186/1471-2164-11-670] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 11/26/2010] [Indexed: 01/13/2023] Open
Abstract
Background The Beijing genotype of M. tuberculosis is a virulent strain that is disseminating worldwide and has a strong association with drug resistance. In the Western Cape of South Africa, epidemiological studies have identified the R220 cluster of the Beijing genotype as a major contributor to a recent outbreak of drug-resistant tuberculosis. Although the outbreak is considered to be due to clonal transmission, the relationship among drug resistant isolates has not yet been established. Results To better understand the evolution of drug resistance among these strains, 14 drug-resistant clinical isolates of the Beijing genotype were sequenced by whole-genome sequencing, including eight from R220 and six from a more ancestral Beijing cluster, R86, for comparison. While each cluster shares a distinct resistance mutation for isoniazid, mapping of other drug-resistance mutations onto a phylogenetic tree constructed from single nucleotide polymorphisms shows that resistance mutations to many drugs have arisen multiple times independently within each cluster of isolates. Thus, drug resistance among these isolates appears to be acquired, not clonally derived. This observation suggests that, although the Beijing genotype as a whole might have selective advantages enabling its rapid dissemination, the XDR isolates are relatively less fit and do not propagate well. Although it has been hypothesized that the increased frequency of drug resistance in some Beijing lineages might be caused by a mutator phenotype, no significant shift in synonymous substitution patterns is observed in the genomes. Conclusion While MDR-TB is spreading by transmission in the Western Cape, our data suggests that further drug resistance (i.e. XDR-TB) at this stage is acquired.
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Affiliation(s)
- Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA.
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19
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Insertion sequences as highly resolutive genomic markers for sequence type 1 Legionella pneumophila Paris. J Clin Microbiol 2010; 49:315-24. [PMID: 20980561 DOI: 10.1128/jcm.01261-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The causative agent of legionellosis, Legionella pneumophila, colonizes all natural and human-made water networks, thus constituting the source of contaminated aerosols responsible for airborne human infections. Efficient control of infections, especially during epidemics, necessitates the fastest and most resolutive identification possible of the bacterial source for subsequent disinfection of reservoirs. We thus compared recognized typing approaches for Legionella with a method based on characterization of insertion sequence (IS) content. A total of 86 clinical or environmental isolates of L. pneumophila, including 84 Paris isolates, sampled from 25 clinical investigations in France between 2001 and 2007, were obtained from the Legionella National Reference Center. All strains were typed by monoclonal antibody subgrouping, sequence-based typing, pulsed-field gel electrophoresis, and restriction fragment length polymorphism based on the presence or absence of IS elements. We identified six different types of IS elements in L. pneumophila Paris and used them as genomic markers in hybridization experiments. One IS type, ISLpn11, revealed a high discriminatory power. Simpson's index of discrimination, calculated from the distribution of IS elements, was higher than that obtained with the other typing methods used for L. pneumophila Paris. Moreover, specific ISLpn11 copies were found only in strains isolated from particular cities. In more than half of the cases, each clinical isolate had an ISLpn11 profile that was recovered in at least one environmental isolate from the same geographical location, suggesting that our method could identify the infection source. Phylogenetic analysis suggests a clonal expansion for the L. pneumophila Paris strain.
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20
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Novel multiplex PCR using dual-priming oligonucleotides for detection and discrimination of the Mycobacterium tuberculosis complex and M. bovis BCG. J Clin Microbiol 2010; 48:4612-4. [PMID: 20943867 DOI: 10.1128/jcm.00872-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We developed a novel multiplex PCR assay using dual-priming oligonucleotide primers targeting the RD1 gene for simultaneous identification of the Mycobacterium tuberculosis complex and M. bovis bacillus Calmette-Guérin (BCG). This assay would be useful both for detection of the M. tuberculosis complex and for differentiation of M. bovis BCG from pathogenic M. tuberculosis complex species.
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21
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Velji P, Nikolayevskyy V, Brown T, Drobniewski F. Discriminatory ability of hypervariable variable number tandem repeat loci in population-based analysis of Mycobacterium tuberculosis strains, London, UK. Emerg Infect Dis 2010; 15:1609-16. [PMID: 19861054 PMCID: PMC2866407 DOI: 10.3201/eid1510.090463] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
To address conflicting results about the stability of variable number tandem repeat (VNTR) loci and their value in prospective molecular epidemiology of Mycobacterium tuberculosis, we conducted a large prospective population-based analysis of all M. tuberculosis strains in a metropolitan setting. Optimal and reproducible conditions for reliable PCR and fragment analysis, comprising enzymes, denaturing conditions, and capillary temperature, were identified for a panel of hypervariable loci, including 3232, 2163a, 1982, and 4052. A total of 2,261 individual M. tuberculosis isolates and 265 sets of serial isolates were analyzed by using a standardized 15-loci VNTR panel, then an optimized hypervariable loci panel. The discriminative ability of loci varied substantially; locus VNTR 3232 varied the most, with 19 allelic variants and Hunter-Gaston index value of 0.909. Hypervariable loci should be included in standardized panels because they can provide consistent comparable results at multiple settings, provided the proposed conditions are adhered to.
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Affiliation(s)
- Preya Velji
- Barts and The London School of Medicine, Queen Mary, University of London, London, UK
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22
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Thong-On A, Smittipat N, Juthayothin T, Yanai H, Yamada N, Yorsangsukkamol J, Chaiprasert A, Rienthong D, Billamas P, Palittapongarnpim P. Variable-number tandem repeats typing of Mycobacterium tuberculosis isolates with low copy numbers of IS6110 in Thailand. Tuberculosis (Edinb) 2010; 90:9-15. [DOI: 10.1016/j.tube.2009.10.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 10/22/2009] [Accepted: 10/22/2009] [Indexed: 11/29/2022]
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Abstract
Although tuberculosis is still a public health problem in Mexico, there is little information about the genetic characteristics of the isolates. In the present study, we analyzed by spoligotyping 180 Mycobacterium tuberculosis clinical isolates from the urban area of Monterrey, Mexico, including drug-susceptible and drug-resistant isolates. The spoligotype patterns were compared with those in the international SITVIT2 spoligotyping database. Four isolates presented spoligotype patterns not found in the database (orphan types); the rest were distributed among 44 spoligo international types (SITs). SIT53 (clade T1) and SIT119 (clade X1) were predominant and included 43 (23.8%) and 28 (15.5%) of the isolates, respectively. In order to determine if there was a dominant spoligotype in the group of multidrug-resistant isolates, 37 of them were analyzed by IS6110-based restriction fragment length polymorphism assays, and scarce clustering of strains with more than five bands was observed. Fourteen isolates of this multidrug-resistant group presented four bands or less and were distributed in four SITs: SIT53 (n = 8), SIT92 (n = 3), SIT70 (n = 2), and SIT3038 (n = 1). When the molecular detection of mutations in the katG and rpoB genes were analyzed in these isolates with low copy numbers of IS6110, only two isolates shared the same IS6110, spoligotyping, and mutations patterns. When the distribution of the spoligotypes was analyzed by age cohort, SIT119 was predominantly found in patients 0 to 20 years old, especially in males, accounting for up to 40% of the isolates. In contrast, SIT53 was more prevalent in older females. This analysis demonstrates the variability of M. tuberculosis isolates in Monterrey and the partial dominance of SIT53 and SIT119 in that area of Mexico.
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24
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McEvoy CRE, Warren RM, van Helden PD, Gey van Pittius NC. Multiple, independent, identical IS6110 insertions in Mycobacterium tuberculosis PPE genes. Tuberculosis (Edinb) 2009; 89:439-42. [PMID: 19734099 DOI: 10.1016/j.tube.2009.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 08/12/2009] [Accepted: 08/16/2009] [Indexed: 11/30/2022]
Abstract
IS6110 is a transposable element found in Mycobacterium tuberculosis complex members. Regions of preferential IS6110 integration occur within the M. tuberculosis genome but the element has not previously been shown to exhibit any sequence-specific integration preferences. Here we provide evidence for multiple independent IS6110 insertions into identical, or near-identical, positions within the highly homologous 5' region of 3 PPE genes.
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Affiliation(s)
- Christopher R E McEvoy
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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25
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van der Spuy GD, Kremer K, Ndabambi SL, Beyers N, Dunbar R, Marais BJ, van Helden PD, Warren RM. Changing Mycobacterium tuberculosis population highlights clade-specific pathogenic characteristics. Tuberculosis (Edinb) 2008; 89:120-5. [PMID: 19054717 DOI: 10.1016/j.tube.2008.09.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 09/29/2008] [Accepted: 09/29/2008] [Indexed: 11/30/2022]
Abstract
Mycobacterium tuberculosis strains can be classified into a number of major clades according to defined evolutionary markers. It is hypothesised that strains comprising these clades have evolved different properties which may influence a local strain population structure. To investigate this, we analysed the incidence of tuberculosis caused by the predominant clades (Beijing, Haarlem, LAM, Quebec and the Low-Copy Clade) found in a community within the Cape Town metropole in South Africa over a 12-year period. We found that while the incidence of cases infected with strains of the Haarlem, LAM, Quebec and the Low-Copy Clades remained relatively stable, that of cases of the Beijing clade increased exponentially over time, with a doubling time of 4.86 years (P=0.018). This growth was exclusively attributable to drug-susceptible strains. Although drug-resistant Beijing cases remained constant in number, non-Beijing drug-resistant cases declined over time (P=0.007). Drug-susceptible Beijing-infected cases had a greater proportion of smear-positive sputa than their non-Beijing counterparts (P=0.013) and were less likely to be successfully treated (retreatment cases) (P=0.026). Recent evidence suggests that these differences likely reflect enhanced pathogenicity rather than transmissibility. The rapid emergence of Beijing strains demonstrates adaptation to conditions within the study community and poses a grave challenge to future TB control.
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Affiliation(s)
- G D van der Spuy
- Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa.
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Discordance between mycobacterial interspersed repetitive-unit-variable-number tandem-repeat typing and IS6110 restriction fragment length polymorphism genotyping for analysis of Mycobacterium tuberculosis Beijing strains in a setting of high incidence of tuberculosis. J Clin Microbiol 2008; 46:3338-45. [PMID: 18716230 DOI: 10.1128/jcm.00770-08] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
IS6110 restriction fragment length polymorphism (RFLP) genotyping is the most widely used genotyping method to study the epidemiology of Mycobacterium tuberculosis. However, due to the complexity of the IS6110 RFLP genotyping technique, and the interpretation of RFLP data, mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) genotyping has been proposed as the new genotyping standard. This study aimed to determine the discriminatory power of different MIRU-VNTR locus combinations relative to IS6110 RFLP genotyping, using a collection of Beijing genotype M. tuberculosis strains with a well-established phylogenetic history. Clustering, diversity index, clustering concordance, concordance among unique genotypes, and divergent and convergent evolution were calculated for seven combinations of 27 different MIRU-VNTR loci and compared to IS6110 RFLP results. Our results confirmed previous findings that MIRU-VNTR genotyping can be used to estimate the extent of recent or ongoing transmission. However, molecular epidemiological linking of cases varied significantly depending on the genotyping method used. We conclude that IS6110 RFLP and MIRU-VNTR loci evolve independently and at different rates, which leads to discordance between transmission chains predicted by the respective genotyping methods. Concordance between the two genotyping methods could be improved by the inclusion of genetic distance (GD) into the clustering formulae for some of the MIRU-VNTR loci combinations. In summary, our findings differ from previous reports, which may be explained by the fact that in settings of low tuberculosis incidence, the genetic distance between epidemiologically unrelated isolates was sufficient to define a strain using either marker, whereas in settings of high incidence, continuous evolution and persistence of strains revealed the weaknesses inherent to these markers.
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Mach M, Grubbs RD, Price WA, Nagaoka M, Dubovický M, Lucot JB. Delayed behavioral and endocrine effects of sarin and stress exposure in mice. J Appl Toxicol 2008; 28:132-9. [PMID: 17503400 DOI: 10.1002/jat.1258] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The organophosphorus agent sarin is a potent inhibitor of acetylcholinesterase. Experiments tested the influence of exposure to low doses of sarin along with psychological stress on delayed behavioral and endocrine changes in mice. Motor activity, acoustic startle response (ASR), pre-pulse inhibition (PPI) of ASR, activity of cholinesterase in blood and catecholamine levels in adrenals were evaluated after low dose sarin exposure (3 x 0.4 LD50 subcutaneously) combined with chronic intermittent stress in C57BL/6J mice. While sarin alone produced depression of motor activity, no interaction of the stress with sarin exposure was observed. Cholinesterase activity was significantly reduced 24 h after exposure to sarin; however, the basal activity was re-established 3 weeks later. The combination of low dose sarin exposure and stress produced delayed behavioral change manifested as excessive grooming together with endocrine alterations in adrenals 7 weeks after exposure. The size of the adrenals in the combined exposure group was increased and the concentration of catecholamines was significantly decreased. In conclusion, these findings indicate that sarin in low doses is more dangerous when combined with shaker stress inducing delayed behavioral and endocrine changes.
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Affiliation(s)
- Mojmir Mach
- Wright State University, Boohnshoft School of Medicine, Dayton, OH 45435, USA.
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28
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Rahim Z, Zaman K, van der Zanden AGM, Möllers MJ, van Soolingen D, Raqib R, Zaman K, Begum V, Rigouts L, Portaels F, Rastogi N, Sola C. Assessment of population structure and major circulating phylogeographical clades of Mycobacterium tuberculosis complex in Bangladesh suggests a high prevalence of a specific subclade of ancient M. tuberculosis genotypes. J Clin Microbiol 2007; 45:3791-4. [PMID: 17804653 PMCID: PMC2168514 DOI: 10.1128/jcm.01247-07] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Revised: 08/09/2007] [Accepted: 08/29/2007] [Indexed: 11/20/2022] Open
Abstract
Spoligotyping was performed to study the population structure of Mycobacterium tuberculosis complex strains (n = 224) from Bangladesh. Strains were split into principal genetic group 1 (PGG 1 [75.0%]) and PGG 2 and 3 (25%). Forty-nine strains with a new spoligotype signature and considered as south or southeast Asian-linked emerging clones were designated as "Matlab type."
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Affiliation(s)
- Zeaur Rahim
- International Centre for Diarrhoeal Disease Research, Bangladesh, Center for Health and Population Research, Dhaka, Bangladesh.
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29
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Wada T, Maeda S, Hase A, Kobayashi K. Evaluation of variable numbers of tandem repeat as molecular epidemiological markers of Mycobacterium tuberculosis in Japan. J Med Microbiol 2007; 56:1052-1057. [PMID: 17644712 DOI: 10.1099/jmm.0.46990-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using 243 Mycobacterium tuberculosis isolates obtained in 2001 in Osaka City, Japan, the discriminatory power of variable numbers of tandem repeats (VNTRs) of 12 standard mycobacterial interspersed repetitive units (MIRUs) was assessed. The biggest cluster defined by MIRU-VNTRs consisted of 57 (23.5 %) isolates and they belonged to the Beijing family based on spoligotyping. When additional VNTR loci were included in the MIRU-VNTR analysis, the 57 originally clustered strains were further differentiated by the addition of Queen's University Belfast (QUB)-VNTRs, but not exact tandem repeat-VNTR. The allelic diversity of additional VNTR loci such as VNTR 3232 (QUB-3232), VNTR 2163a (QUB-11a), VNTR 2163b (QUB-11b) and VNTR 1982 (QUB-18) was high in the 57 strains. When the 243 M. tuberculosis isolates were analysed using 16-locus VNTR (the 12 standard MIRUs and the 4 QUB loci) and IS6110 RFLP, the respective Hunter-Gaston discriminatory indexes were 0.9966 and 0.9971. The discrimination power of 16-locus VNTR was equal to that of IS6110 RFLP analysis. If appropriate loci are added to the standard MIRU analysis, VNTR genotyping could be a valuable tool for strain typing and epidemiological research of M. tuberculosis in Japan.
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Affiliation(s)
- Takayuki Wada
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Shinji Maeda
- Molecular Epidemiology and Genetic Identification, Mycobacterium Reference Center, Research Institute of Tuberculosis, 3-1-24 Matsuyama, Kiyose, Tokyo 204-8533, Japan
| | - Atsushi Hase
- Department of Microbiology, Osaka City Institute of Public Health and Environmental Sciences, 8-34 Tojo-cho, Tennoji-ku, Osaka 543-0026, Japan
| | - Kazuo Kobayashi
- Department of Immunology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan
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Ali A, Hasan Z, Tanveer M, Siddiqui AR, Ghebremichael S, Kallenius G, Hasan R. Characterization of Mycobacterium tuberculosis Central Asian Strain 1 using mycobacterial interspersed repetitive unit genotyping. BMC Microbiol 2007; 7:76. [PMID: 17686185 PMCID: PMC1988810 DOI: 10.1186/1471-2180-7-76] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 08/09/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Central Asian Strain 1 (CAS1) genogroup of Mycobacterium tuberculosis (MTB) is the most prevalent in Pakistan, India and Bangladesh. Mycobacterial interspersed repetitive units variable number tandem repeat (MIRU-VNTR) typing is a reliable and reproducible method for differentiation of MTB isolates. However, information of its utility in determining the diversity of CAS1 strain is limited. We performed standard 12 loci based MIRU-VNTR typing on previously spoligotyped CAS1 strains and 'unique' strains in order to evaluate its discriminatory power for these isolates. METHODS Twelve loci based MIRU- VNTR typing was used to type 178 CAS1 and 189 'unique' MTB strains. The discriminatory index for each of the loci was calculated using the Hunter Gaston Discriminatory Index (HGDI). A subset of these strains (n = 78) were typed using IS6110 restriction fragment length polymorphism (RFLP). MIRU-VNTR profiles were studied together with their drug susceptibility patterns. RESULTS A total of 349 MIRU patterns were obtained for the 367 strains tested. The CAS1 strains were subdivided into 160 distinct patterns; 15 clusters of 2 strains each, 1 cluster of four strains and 144 unique patterns. Using HGDI, seven MIRU loci, (numbers 26, 31, 27, 16, 10, 39, and 40) were found to be "highly discriminatory" (DI: >or=0.6), four MIRU loci (numbers 20, 24, 23, and 4) were "moderately discriminatory" (DI: 0.3-0.59), and one locus (number 2) was "poorly discriminatory" (DI< 0.3). Loci 26 and 31 were the most discriminatory for the CAS1 isolates. Amongst 'unique' strains in addition to loci 26, 31, 27, 16, 10, 39, and 40, locus 23 was highly discriminatory, while no locus was poorly discriminating. DI values for loci 4, 10 and 26 were significantly lower (P-value < .01) in CAS1 strains than in 'unique' strains. The association between CAS1 strains and MDR was not found to be significant (p value = 0.21). CONCLUSION We propose that MIRU typing could be used to estimate the phylogenetic relatedness amongst prevalent CAS1 strains, for which MIRU loci 26, 31, 16, 10, 27, 39 and 40 were found to be the most discriminatory.
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Affiliation(s)
- Asho Ali
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road, PO Box 3500, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road, PO Box 3500, Karachi, Pakistan
| | - Mahnaz Tanveer
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road, PO Box 3500, Karachi, Pakistan
| | - Amna R Siddiqui
- Department of Community Health Sciences, The Aga Khan University, Stadium Road, PO Box 3500, Karachi, Pakistan
| | - Solomon Ghebremichael
- Department of Bacteriology, Swedish Institute for Infectious Diseases Control, Stockholm, Sweden
| | - Gunilla Kallenius
- Department of Bacteriology, Swedish Institute for Infectious Diseases Control, Stockholm, Sweden
- Microbiology and Tumor Cell Biology, Karolinska Institute, Nobels Vag 16, Stockholm, Sweden
| | - Rumina Hasan
- Department of Pathology and Microbiology, The Aga Khan University, Stadium Road, PO Box 3500, Karachi, Pakistan
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Gutierrez MC, Ahmed N, Willery E, Narayanan S, Hasnain SE, Chauhan DS, Katoch VM, Vincent V, Locht C, Supply P. Predominance of ancestral lineages of Mycobacterium tuberculosis in India. Emerg Infect Dis 2006; 12:1367-74. [PMID: 17073085 PMCID: PMC3294724 DOI: 10.3201/eid1209.050017] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular epidemiologic findings suggest an ancient focus of TB. Although India has the highest prevalence of tuberculosis (TB) worldwide, the genetic diversity of Mycobacterium tuberculosis in India is largely unknown. A collection of 91 isolates originating from 12 different regions spread across the country were analyzed by genotyping using 21 loci with variable-number tandem repeats (VNTRs), by spoligotyping, by principal genetic grouping (PGG), and by deletion analysis of M. tuberculosis–specific deletion region 1. The isolates showed highly diverse VNTR genotypes. Nevertheless, highly congruent groupings identified by using the 4 independent sets of markers permitted a clear definition of 3 prevalent PGG1 lineages, which corresponded to the "ancestral" East African–Indian, the Delhi, and the Beijing/W genogroups. A few isolates from PGG2 lineages and a single representative of the presumably most recent PGG3 were identified. These observations suggest a predominance of ancestral M. tuberculosis genotypes in the Indian subcontinent, which supports the hypothesis that India is an ancient endemic focus of TB.
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Affiliation(s)
| | - Niyaz Ahmed
- Center for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | | | | | | | - Devendra S. Chauhan
- National Jalma Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
| | - Vishwa M. Katoch
- National Jalma Institute for Leprosy and Other Mycobacterial Diseases, Agra, India
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Streicher EM, Victor TC, van der Spuy G, Sola C, Rastogi N, van Helden PD, Warren RM. Spoligotype signatures in the Mycobacterium tuberculosis complex. J Clin Microbiol 2006; 45:237-40. [PMID: 17065260 PMCID: PMC1828946 DOI: 10.1128/jcm.01429-06] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Evolution of the direct repeat region in Mycobacterium tuberculosis has created unique spoligotype signatures specifically associated with IS6110-defined strain families. Spoligotyping signatures may enable the analysis of the strain population structure in different settings and will enable the rapid identification of strain families that acquire drug resistance or escape protective immunity in drug and vaccine trials.
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Affiliation(s)
- E M Streicher
- DST/NRF Centre of Excellence in Biomedical TB Research, Department of Medical Biochemistry, Stellenbosch University, Tygerberg, South Africa 7505
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Mathema B, Kurepina NE, Bifani PJ, Kreiswirth BN. Molecular epidemiology of tuberculosis: current insights. Clin Microbiol Rev 2006; 19:658-85. [PMID: 17041139 PMCID: PMC1592690 DOI: 10.1128/cmr.00061-05] [Citation(s) in RCA: 236] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular epidemiologic studies of tuberculosis (TB) have focused largely on utilizing molecular techniques to address short- and long-term epidemiologic questions, such as in outbreak investigations and in assessing the global dissemination of strains, respectively. This is done primarily by examining the extent of genetic diversity of clinical strains of Mycobacterium tuberculosis. When molecular methods are used in conjunction with classical epidemiology, their utility for TB control has been realized. For instance, molecular epidemiologic studies have added much-needed accuracy and precision in describing transmission dynamics, and they have facilitated investigation of previously unresolved issues, such as estimates of recent-versus-reactive disease and the extent of exogenous reinfection. In addition, there is mounting evidence to suggest that specific strains of M. tuberculosis belonging to discrete phylogenetic clusters (lineages) may differ in virulence, pathogenesis, and epidemiologic characteristics, all of which may significantly impact TB control and vaccine development strategies. Here, we review the current methods, concepts, and applications of molecular approaches used to better understand the epidemiology of TB.
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Affiliation(s)
- Barun Mathema
- Tuberculosis Center, Public Health Research Institute, Newark, NJ 07103, USA.
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Supply P, Allix C, Lesjean S, Cardoso-Oelemann M, Rüsch-Gerdes S, Willery E, Savine E, de Haas P, van Deutekom H, Roring S, Bifani P, Kurepina N, Kreiswirth B, Sola C, Rastogi N, Vatin V, Gutierrez MC, Fauville M, Niemann S, Skuce R, Kremer K, Locht C, van Soolingen D. Proposal for standardization of optimized mycobacterial interspersed repetitive unit-variable-number tandem repeat typing of Mycobacterium tuberculosis. J Clin Microbiol 2006; 44:4498-510. [PMID: 17005759 PMCID: PMC1698431 DOI: 10.1128/jcm.01392-06] [Citation(s) in RCA: 1002] [Impact Index Per Article: 55.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular typing based on 12 loci containing variable numbers of tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTRs) has been adopted in combination with spoligotyping as the basis for large-scale, high-throughput genotyping of Mycobacterium tuberculosis. However, even the combination of these two methods is still less discriminatory than IS6110 fingerprinting. Here, we define an optimized set of MIRU-VNTR loci with a significantly higher discriminatory power. The resolution and the stability/robustness of 29 loci were analyzed, using a total of 824 tubercle bacillus isolates, including representatives of the main lineages identified worldwide so far. Five loci were excluded for lack of robustness and/or stability in serial isolates or isolates from epidemiologically linked patients. The use of the 24 remaining loci increased the number of types by 40%--and by 23% in combination with spoligotyping--among isolates from cosmopolitan origins, compared to those obtained with the original set of 12 loci. Consequently, the clustering rate was decreased by fourfold--by threefold in combination with spoligotyping--under the same conditions. A discriminatory subset of 15 loci with the highest evolutionary rates was then defined that concentrated 96% of the total resolution obtained with the full 24-locus set. Its predictive value for evaluating M. tuberculosis transmission was found to be equal to that of IS6110 restriction fragment length polymorphism typing, as shown in a companion population-based study. This 15-locus system is therefore proposed as the new standard for routine epidemiological discrimination of M. tuberculosis isolates and the 24-locus system as a high-resolution tool for phylogenetic studies.
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Affiliation(s)
- Philip Supply
- INSERM U629, Institut Pasteur de Lille, 1, rue du Prof. Calmette, F-59019 Lille Cedex, France.
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Arnold C, Thorne N, Underwood A, Baster K, Gharbia S. Evolution of short sequence repeats in Mycobacterium tuberculosis. FEMS Microbiol Lett 2006; 256:340-6. [PMID: 16499626 DOI: 10.1111/j.1574-6968.2006.00142.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Whole genome comparison has revealed the presence of short sequence repeats (also called mycobacterial interspersed repeat units and variable number tandem repeat units) used for genotyping schemes. In this study, we have used deletion analysis, single nucleotide polymorphism data and spoligotype taken from published data from others to investigate the evolution of selected repeats that form the common denominators of the majority of established schemes. Analysis of the number of repeats per locus from over 400 isolates revealed that the general trend globally appears to be loss of repeats in modern strains compared with ancestral strains.
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Affiliation(s)
- Cath Arnold
- Centre for Infections, Health Protection Agency, London, UK.
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36
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Shamputa IC, Jugheli L, Sadradze N, Willery E, Portaels F, Supply P, Rigouts L. Mixed infection and clonal representativeness of a single sputum sample in tuberculosis patients from a penitentiary hospital in Georgia. Respir Res 2006; 7:99. [PMID: 16846493 PMCID: PMC1538999 DOI: 10.1186/1465-9921-7-99] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Accepted: 07/17/2006] [Indexed: 11/23/2022] Open
Abstract
Background Studies on recurrent tuberculosis (TB), TB molecular epidemiology and drug susceptibility testing rely on the analysis of one Mycobacterium tuberculosis isolate from a single sputum sample collected at different disease episodes. This scheme rests on the postulate that a culture of one sputum sample is homogeneous and representative of the total bacillary population in a patient. Methods We systematically analysed several pre-treatment isolates from each of 199 smear-positive male adult inmates admitted to a prison TB hospital by standard IS6110 DNA fingerprinting, followed by PCR typing based on multiple loci containing variable number of tandem repeats (VNTRs) on a subset of isolates. Drug susceptibility testing (DST) was performed on all isolates for isoniazid, rifampicin, streptomycin and ethambutol. Results We found mixed infection in 26 (13.1%) cases. In contrast, analysis of a single pre-treatment isolate per patient would have led to missed mixed infections in all or 14 of these 26 cases by using only standard DNA fingerprinting or the PCR multilocus-based method, respectively. Differences in DST among isolates from the same patient were observed in 10 cases, of which 6 were from patients with mixed infection. Conclusion These results suggest that the actual heterogeneity of the bacillary population in patients, especially in high TB incidence settings, may be frequently underestimated using current analytical schemes. These findings have therefore important implications for correct interpretation and evaluation of molecular epidemiology data and in treatment evaluations.
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Affiliation(s)
- Isdore C Shamputa
- Prince Leopold Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, B-2000 Antwerp, Belgium
- Tropical Diseases Research Centre, Microbiology Unit, P. O. Box 71769, Ndola, Zambia
| | - Levan Jugheli
- Prince Leopold Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, B-2000 Antwerp, Belgium
- International Committee of the Red Cross, 4, Kedia Str. 380054, Tbilisi, Georgia
| | - Nikoloz Sadradze
- International Committee of the Red Cross, 4, Kedia Str. 380054, Tbilisi, Georgia
| | - Eve Willery
- Laboratoire des Mécanismes Moléculaires de la Pathogenèse Bactérienne, INSERM U629, Institut de Biologie/Institut Pasteur de Lille, Lille, France
| | - Françoise Portaels
- Prince Leopold Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, B-2000 Antwerp, Belgium
| | - Philip Supply
- Laboratoire des Mécanismes Moléculaires de la Pathogenèse Bactérienne, INSERM U629, Institut de Biologie/Institut Pasteur de Lille, Lille, France
| | - Leen Rigouts
- Prince Leopold Institute of Tropical Medicine, Mycobacteriology Unit, Nationalestraat 155, B-2000 Antwerp, Belgium
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37
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Brudey K, Driscoll JR, Rigouts L, Prodinger WM, Gori A, Al-Hajoj SA, Allix C, Aristimuño L, Arora J, Baumanis V, Binder L, Cafrune P, Cataldi A, Cheong S, Diel R, Ellermeier C, Evans JT, Fauville-Dufaux M, Ferdinand S, de Viedma DG, Garzelli C, Gazzola L, Gomes HM, Guttierez MC, Hawkey PM, van Helden PD, Kadival GV, Kreiswirth BN, Kremer K, Kubin M, Kulkarni SP, Liens B, Lillebaek T, Ly HM, Martin C, Martin C, Mokrousov I, Narvskaïa O, Ngeow YF, Naumann L, Niemann S, Parwati I, Rahim Z, Rasolofo-Razanamparany V, Rasolonavalona T, Rossetti ML, Rüsch-Gerdes S, Sajduda A, Samper S, Shemyakin IG, Singh UB, Somoskovi A, Skuce RA, van Soolingen D, Streicher EM, Suffys PN, Tortoli E, Tracevska T, Vincent V, Victor TC, Warren RM, Yap SF, Zaman K, Portaels F, Rastogi N, Sola C. Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology. BMC Microbiol 2006; 6:23. [PMID: 16519816 PMCID: PMC1468417 DOI: 10.1186/1471-2180-6-23] [Citation(s) in RCA: 777] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 03/06/2006] [Indexed: 12/04/2022] Open
Abstract
Background The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. Results The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. Conclusion Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.
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Affiliation(s)
- Karine Brudey
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | | | - Leen Rigouts
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Wolfgang M Prodinger
- Dept. Hygiene Microbiology and Social Medicine, Innsbruck Medical University, Innsbruck, Austria
| | - Andrea Gori
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Sahal A Al-Hajoj
- Department of Comparative Medicine, King Faisal specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Caroline Allix
- Laboratoire de la Tuberculose, Institut Pasteur de Bruxelles, Belgique
| | - Liselotte Aristimuño
- Universidad Centrooccidental Lisandro Alvarado, Barquisimeto, Venezuela and Universidad de Zaragoza, Spain
| | - Jyoti Arora
- All India Institute of Medical Sciences, New Delhi, India
| | | | - Lothar Binder
- Institut for Hygiene, Microbiologie and Tropical Medicine, Austria
| | | | - Angel Cataldi
- Instituto de Biotecnologia INTA, Castelar, Argentina
| | - Soonfatt Cheong
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Roland Diel
- University of Düsseldorf, Heinrich-Heine-University, Düsseldorf
| | | | - Jason T Evans
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | | | - Séverine Ferdinand
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Dario Garcia de Viedma
- Dept of Clinical Microbiology and Infectious Diseases, Hospital Gregorio Marañon, Madrid, Spain
| | - Carlo Garzelli
- Dept. of Experimental Pathology, Medical Biotechnology, Infection and Epidemiology, Pisa University, Pisa, Italy
| | - Lidia Gazzola
- Dept of Infectious Diseases, Institut of Infectious Diseases, Milano, Italy
| | - Harrison M Gomes
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Peter M Hawkey
- Public Health Laboratory, Hearltlands Hospital, Birmingham, UK
| | - Paul D van Helden
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Gurujaj V Kadival
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | | | - Kristin Kremer
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Milan Kubin
- Municipal Institute of Hygiene, Prague, Czech Republic
| | - Savita P Kulkarni
- Laboratory Nuclear Medicine Section, Isotope group, Bhabha Atomic Research Centre c/T.M.H. Annexe, Parel, Mumbai-400012, India
| | - Benjamin Liens
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Troels Lillebaek
- Statens Serum Institute, Int. Ref. lab. for Mycobacteriology, Copenhagen Denmark
| | - Ho Minh Ly
- Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Christian Martin
- Laboratoire de Bactério-virologie-hygiène, CHU Dupuytren, Limoges, France
| | - Igor Mokrousov
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Olga Narvskaïa
- Institut Pasteur de Saint-Petersbourg, Saint Petersbourg, Russia
| | - Yun Fong Ngeow
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Ludmilla Naumann
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Stefan Niemann
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Ida Parwati
- Dept of Clinical Pathology, Padjadjaran University, Dr. Hasan Sadikin Hospital, Bandung, Indonesia
| | - Zeaur Rahim
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | | | | | | | - Sabine Rüsch-Gerdes
- Forschungszentrum, National Reference Center for Mycobacteria, Borstel, Germany
| | - Anna Sajduda
- Dept of Genetics of Microorganisms, University of Lódz, Lodz, Poland
| | - Sofia Samper
- Servicio Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Igor G Shemyakin
- State Research Center for Applied Microbiology, Obolensk, Russian Federation
| | | | - Akos Somoskovi
- Dept. of Respiratory Medicine School of Medicine Semmelweis University, Budapest, Hungary
| | - Robin A Skuce
- Veterinary Sciences Division, Department of agriculture for Northern Ireland, Belfast, UK
| | - Dick van Soolingen
- Mycobacteria reference unit, Diagnostic Laboratory for Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth M Streicher
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Philip N Suffys
- Laboratory of Molecular Biology applied to Mycobacteria, Dept. Mycobacteriosis, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | - Enrico Tortoli
- Centro regionale di Riferimento per i Micobatteri, Laboratorio de Microbiologia e Virologia, Ospedale Careggi, Firenze, Italy
| | | | - Véronique Vincent
- Centre National de Référence des Mycobactéries, Institut Pasteur, Paris, France
| | - Tommie C Victor
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Robin M Warren
- MRC Centre for Molecular and Cellular Biology, Dept of medical Biochemistry, University of Stellenbosch, Tygerberg, South Africa
| | - Sook Fan Yap
- Dept of Medical Microbiology and Pathology, faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia, School of Public Health
| | - Khadiza Zaman
- Tuberculosis Laboratory, International Centre for Diarrhoeal Research, Dhaka, Bangladesh
| | - Françoise Portaels
- Mycobacteriology Unit, Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Nalin Rastogi
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
| | - Christophe Sola
- Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de Guadeloupe, Guadeloupe
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van Deutekom H, Supply P, de Haas PEW, Willery E, Hoijng SP, Locht C, Coutinho RA, van Soolingen D. Molecular typing of Mycobacterium tuberculosis by mycobacterial interspersed repetitive unit-variable-number tandem repeat analysis, a more accurate method for identifying epidemiological links between patients with tuberculosis. J Clin Microbiol 2005; 43:4473-9. [PMID: 16145094 PMCID: PMC1234145 DOI: 10.1128/jcm.43.9.4473-4479.2005] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
IS6110 fingerprinting of Mycobacterium tuberculosis is the standard identification method in studies on transmission of tuberculosis. However, intensive epidemiological investigation may fail to confirm transmission links between patients clustered by IS6110-restriction fragment length polymorphism (RFLP) typing. We applied typing based on variable numbers of tandem repeats (VNTRs) of mycobacterial interspersed repetitive units (MIRUs) to isolates from 125 patients in 42 IS6110 clusters, for which thorough epidemiological data were available, to investigate the potential of this method in distinguishing epidemiologically linked from nonlinked patients. Of seven IS6110 clusters without epidemiological links, five were split by MIRU-VNTR typing, while nearly all IS6110 clusters with proven or likely links displayed conserved MIRU-VNTR types. These results provide molecular evidence that not all clusters determined on the basis of multibanded IS6110 RFLP patterns necessarily reflect transmission of tuberculosis. They support the use of MIRU-VNTR typing as a more reliable and faster method for transmission analysis.
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Affiliation(s)
- Henk van Deutekom
- Department of Tuberculosis Control, Municipal Health Service, Amsterdam, The Netherlands.
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Sarojini S, Soman S, Radhakrishnan I, Mundayoor S. Identification of moaA3 gene in patient isolates of Mycobacterium tuberculosis in Kerala, which is absent in M. tuberculosis H37Rv and H37Ra. BMC Infect Dis 2005; 5:81. [PMID: 16202156 PMCID: PMC1262720 DOI: 10.1186/1471-2334-5-81] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2005] [Accepted: 10/04/2005] [Indexed: 11/10/2022] Open
Abstract
Background Tuberculosis is endemic to developing countries like India. Though the whole genome sequences of the type strain M. tuberculosis H37Rv and the clinical strain M. tuberculosis CDC1551 are available, the clinical isolates from India have not been studied extensively at the genome level. This study was carried out in order to have a better understanding of isolates from Kerala, a state in southern India. Results A PCR based strategy was followed making use of the deletion region primers to understand the genome level differences between the type strain H37Rv and the clinical isolates of M. tuberculosis from Kerala. PCR analysis of patient isolates using RD1 region primers revealed the amplification of a 386 bp region, in addition to the expected 652 bp amplicon. Southern hybridization of genomic DNA with the 386 bp amplicon confirmed the presence of this new region in a majority of the patient isolates from Kerala. Sequence comparison of this amplicon showed close homology with the moaA3 gene of M. bovis. In M. bovis this gene is present in the RvD5 region, an IS6110 mediated deletion that is absent in M. tuberculosis H37Rv. Conclusion This study demonstrates the presence of moaA3 gene, that is absent in M. tuberculosis H37Rv and H37Ra, in a large number of local isolates. Whether the moaA3 gene provides any specific advantage to the field isolates of the pathogen is unclear. Field strains from Kerala have fewer IS6110 sequences and therefore are likely to have fewer IS6110 dependent rearrangements. But as deletions and insertions account for much of the genomic diversity of M. tuberculosis, the mechanisms of formation of sequence polymorphisms in the local isolates should be further examined. These results suggest that studies should focus on strains from endemic areas to understand the complexities of this pathogen.
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Affiliation(s)
- Suma Sarojini
- Mycobacterial Research Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Smitha Soman
- Mycobacterial Research Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Indulakshmi Radhakrishnan
- Mycobacterial Research Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
| | - Sathish Mundayoor
- Mycobacterial Research Group, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India
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Lindstedt BA. Multiple-locus variable number tandem repeats analysis for genetic fingerprinting of pathogenic bacteria. Electrophoresis 2005; 26:2567-82. [PMID: 15937984 DOI: 10.1002/elps.200500096] [Citation(s) in RCA: 244] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA fingerprinting has attracted considerable interest as means for identifying, tracing and preventing the dissemination of infectious agents. Various methods have been developed for typing of pathogenic bacteria, which differ in discriminative power, reproducibility and ease of interpretation. During recent years a typing method, which uses the information provided by whole genome sequencing of bacterial species, has gained increased attention. Short sequence repeat (SSR) motifs are known to undergo frequent variation in the number of repeated units through cellular mechanisms most commonly active during chromosome replication. A class of SSRs, named variable number of tandem repeats (VNTRs), has proven to be a suitable target for assessing genetic polymorphisms within bacterial species. This review attempts to give an overview of bacterial agents where VNTR-based typing, or multiple-locus variant-repeat analysis (MLVA) has been developed for typing purposes, together with addressing advantages and drawbacks associated with the use of tandem repeated DNA motifs as targets for bacterial typing and identification.
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Affiliation(s)
- Bjørn-Arne Lindstedt
- Norwegian Institute of Public Health, Division for Infectious Diseases Control, Oslo, Norway.
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Shamputa IC, Rigouts L, Eyongeta LA, El Aila NA, van Deun A, Salim AH, Willery E, Locht C, Supply P, Portaels F. Genotypic and phenotypic heterogeneity among Mycobacterium tuberculosis isolates from pulmonary tuberculosis patients. J Clin Microbiol 2005; 42:5528-36. [PMID: 15583277 PMCID: PMC535260 DOI: 10.1128/jcm.42.12.5528-5536.2004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the heterogeneity of Mycobacterium tuberculosis populations and the existence of mixed infections are now generally accepted, systematic studies on their relative importance are rare. In the present study, 10 individual colonies of each M. tuberculosis isolate (primary isolate) from 97 tuberculosis patients in a primarily human immunodeficiency virus-negative population were screened for heterogeneity and detectable mixed infections by spoligotyping, IS6110-based restriction fragment length polymorphism analysis, and mycobacterial interspersed repetitive unit-variable number of tandem repeat typing. The MICs of antituberculosis drugs for colonies with divergent fingerprints were determined. Infections with different bacterial subpopulations were detected in the samples from eight patients (8.2%), and the frequency of detectable mixed infections in the study population was estimated to be 2.1%. Genotypic variations were found to be independent of the drug susceptibilities, and the various molecular markers evolved independently in most cases. The predominant strains and the primary isolates always had concordant drug susceptibility and MIC testing results. These findings have implications on the interpretation of molecular epidemiology results for patient follow-up and in transmission studies.
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Affiliation(s)
- Isdore Chola Shamputa
- Mycobacteriology Unit, Department of Microbiology, Prince Leopold Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium.
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